PLK2
polo like kinase 2
Basic information
Region (hg38): 5:58453982-58460139
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Hereditary breast ovarian cancer syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLK2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 16 | 17 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 1 | 0 | 17 | 1 | 1 |
Variants in PLK2
This is a list of pathogenic ClinVar variants found in the PLK2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-58454639-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 5-58454681-T-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 5-58454701-T-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 5-58454993-A-G | Likely benign (May 16, 2018) | |||
| 5-58455557-C-T | not specified | Uncertain significance (Nov 27, 2023) | ||
| 5-58455560-A-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 5-58455591-C-T | not specified | Uncertain significance (Jul 17, 2023) | ||
| 5-58455729-G-A | not specified | Uncertain significance (Aug 13, 2021) | ||
| 5-58456110-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 5-58456583-A-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 5-58456971-T-C | not specified | Uncertain significance (Mar 23, 2023) | ||
| 5-58457052-G-A | Esophageal atresia;Pyloric stenosis | Uncertain significance (May 22, 2019) | ||
| 5-58457184-C-CA | Hereditary breast ovarian cancer syndrome | Pathogenic (Aug 01, 2020) | ||
| 5-58457290-G-A | not specified | Uncertain significance (Nov 28, 2023) | ||
| 5-58457332-T-C | not specified | Uncertain significance (Apr 20, 2023) | ||
| 5-58458110-C-T | Benign (Apr 04, 2018) | |||
| 5-58458477-G-A | Uncertain significance (Feb 01, 2024) | |||
| 5-58458808-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 5-58459076-C-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 5-58459799-G-A | not specified | Uncertain significance (Jul 19, 2023) | ||
| 5-58459809-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
| 5-58459856-G-A | not specified | Uncertain significance (Jul 05, 2023) | ||
| 5-58459926-C-T | not specified | Uncertain significance (Nov 08, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLK2 | protein_coding | protein_coding | ENST00000274289 | 14 | 6279 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000984 | 125721 | 0 | 4 | 125725 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.01 | 207 | 370 | 0.559 | 0.0000178 | 4530 |
| Missense in Polyphen | 69 | 171.09 | 0.40329 | 2146 | ||
| Synonymous | -1.16 | 155 | 138 | 1.13 | 0.00000702 | 1270 |
| Loss of Function | 5.17 | 2 | 35.0 | 0.0571 | 0.00000175 | 425 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Tumor suppressor serine/threonine-protein kinase involved in synaptic plasticity, centriole duplication and G1/S phase transition. Polo-like kinases act by binding and phosphorylating proteins are that already phosphorylated on a specific motif recognized by the POLO box domains. Phosphorylates CENPJ, NPM1, RAPGEF2, RASGRF1, SNCA, SIPA1L1 and SYNGAP1. Plays a key role in synaptic plasticity and memory by regulating the Ras and Rap protein signaling: required for overactivity-dependent spine remodeling by phosphorylating the Ras activator RASGRF1 and the Rap inhibitor SIPA1L1 leading to their degradation by the proteasome. Conversely, phosphorylates the Rap activator RAPGEF2 and the Ras inhibitor SYNGAP1, promoting their activity. Also regulates synaptic plasticity independently of kinase activity, via its interaction with NSF that disrupts the interaction between NSF and the GRIA2 subunit of AMPARs, leading to a rapid rundown of AMPAR-mediated current that occludes long term depression. Required for procentriole formation and centriole duplication by phosphorylating CENPJ and NPM1, respectively. Its induction by p53/TP53 suggests that it may participate in the mitotic checkpoint following stress. {ECO:0000269|PubMed:15242618, ECO:0000269|PubMed:19001868, ECO:0000269|PubMed:20352051, ECO:0000269|PubMed:20531387}.;
- Pathway
- FoxO signaling pathway - Homo sapiens (human);Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;TP53 Regulates Transcription of Cell Cycle Genes;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.0433
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.88
Haploinsufficiency Scores
- pHI
- 0.341
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.579
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Plk2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; skeleton phenotype; vision/eye phenotype;
Zebrafish Information Network
- Gene name
- plk2b
- Affected structure
- dorsal longitudinal anastomotic vessel
- Phenotype tag
- abnormal
- Phenotype quality
- aplastic/hypoplastic
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;protein phosphorylation;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;mitotic spindle organization;mitotic cell cycle checkpoint;Ras protein signal transduction;memory;positive regulation of autophagy;negative regulation of angiogenesis;peptidyl-serine phosphorylation;positive regulation of protein binding;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;Rap protein signal transduction;negative regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of protein catabolic process;regulation of centriole replication;regulation of synaptic plasticity;long-term synaptic potentiation;long-term synaptic depression;negative regulation of dendritic spine development;negative regulation of apoptotic process in bone marrow cell;positive regulation of cell migration involved in sprouting angiogenesis;negative regulation of cellular senescence
- Cellular component
- chromatin;cytoplasm;centrosome;centriole;cytosol;dendrite
- Molecular function
- protein serine/threonine kinase activity;protein binding;ATP binding;ATP-dependent protein binding;protein-containing complex binding